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PLoS One. 2014 Sep 5;9(9):e106649. doi: 10.1371/journal.pone.0106649. eCollection 2014.

Two low coverage bird genomes and a comparison of reference-guided versus de novo genome assemblies.

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Department of Biology, The University of Texas at Arlington, Arlington, Texas, United States of America.
United States Geological Survey - Fort Collins Science Center, Fort Collins, Colorado, United States of America.
Department of Integrative Biology, University of Colorado Denver, Denver, Colorado, United States of America.
Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado, United States of America.


As a greater number and diversity of high-quality vertebrate reference genomes become available, it is increasingly feasible to use these references to guide new draft assemblies for related species. Reference-guided assembly approaches may substantially increase the contiguity and completeness of a new genome using only low levels of genome coverage that might otherwise be insufficient for de novo genome assembly. We used low-coverage (∼3.5-5.5x) Illumina paired-end sequencing to assemble draft genomes of two bird species (the Gunnison Sage-Grouse, Centrocercus minimus, and the Clark's Nutcracker, Nucifraga columbiana). We used these data to estimate de novo genome assemblies and reference-guided assemblies, and compared the information content and completeness of these assemblies by comparing CEGMA gene set representation, repeat element content, simple sequence repeat content, and GC isochore structure among assemblies. Our results demonstrate that even lower-coverage genome sequencing projects are capable of producing informative and useful genomic resources, particularly through the use of reference-guided assemblies.

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